John Quackenbush

  • Dana-Farber Cancer Institute, Boston, USA

According to our database1, John Quackenbush authored at least 67 papers between 2000 and 2022.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.



In proceedings 
PhD thesis 


Online presence:



Looking back at the first twenty years of genomics.
Quant. Biol., 2022

GRAND: a database of gene regulatory network models across human conditions.
Nucleic Acids Res., 2022

Scaling up Continuous-Time Markov Chains Helps Resolve Underspecification.
Proceedings of the Advances in Neural Information Processing Systems 34: Annual Conference on Neural Information Processing Systems 2021, 2021

Gene Regulatory Network Inference as Relaxed Graph Matching.
Proceedings of the Thirty-Fifth AAAI Conference on Artificial Intelligence, 2021

Cascade Size Distributions: Why They Matter and How to Compute Them Efficiently.
Proceedings of the Thirty-Fifth AAAI Conference on Artificial Intelligence, 2021

PUMA: PANDA Using MicroRNA Associations.
Bioinform., 2020

Clustering Sparse Data With Feature Correlation With Application to Discover Subtypes in Cancer.
IEEE Access, 2020

A Novel Deep Learning Model by Stacking Conditional Restricted Boltzmann Machine and Deep Neural Network.
Proceedings of the KDD '20: The 26th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2020

Catalysis Clustering with GAN by Incorporating Domain Knowledge.
Proceedings of the KDD '20: The 26th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2020

Cascade Size Distributions and Why They Matter.
CoRR, 2019

Identification of differentially expressed gene sets using the Generalized Berk-Jones statistic.
Bioinform., 2019

Session introduction.
Proceedings of the Biocomputing 2019: Proceedings of the Pacific Symposium, 2019

Clustering on Sparse Data in Non-overlapping Feature Space with Applications to Cancer Subtyping.
Proceedings of the IEEE International Conference on Data Mining, 2018

Network-based Distance Metric with Application to Discover Disease Subtypes in Cancer.
CoRR, 2017

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data.
BMC Bioinform., 2017

Biomarker correlation network in colorectal carcinoma by tumor anatomic location.
BMC Bioinform., 2017

Estimating gene regulatory networks with pandaR.
Bioinform., 2017

Bipartite Community Structure of eQTLs.
PLoS Comput. Biol., 2016

Safikhani <i>et al</i>. reply.
Nat., 2016

BatchQC: interactive software for evaluating sample and batch effects in genomic data.
Bioinform., 2016

PyPanda: a Python package for gene regulatory network reconstruction.
Bioinform., 2016

Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators.
BMC Syst. Biol., 2015

A network model for angiogenesis in ovarian cancer.
BMC Bioinform., 2015

High performance computing of gene regulatory networks using a message-passing model.
Proceedings of the 2015 IEEE High Performance Extreme Computing Conference, 2015

Sexually-dimorphic targeting of functionally-related genes in COPD.
BMC Syst. Biol., 2014

Analyzing networks of phenotypes in complex diseases: methodology and applications in COPD.
BMC Syst. Biol., 2014

Significance Analysis of Prognostic Signatures.
PLoS Comput. Biol., 2013

Inconsistency in large pharmacogenomic studies.
Nat., 2013

Research and applications: Comparison and validation of genomic predictors for anticancer drug sensitivity.
J. Am. Medical Informatics Assoc., 2013

RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface.
Bioinform., 2013

Viral Perturbations of Host Networks Reflect Disease Etiology.
PLoS Comput. Biol., 2012

Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks.
Nucleic Acids Res., 2012

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures.
Nucleic Acids Res., 2012

iBBiG: iterative binary bi-clustering of gene sets.
Bioinform., 2012

nEASE: a method for gene ontology subclassification of high-throughput gene expression data.
Bioinform., 2012

GCOD - GeneChip Oncology Database.
BMC Bioinform., 2011

Multiple-input multiple-output causal strategies for gene selection.
BMC Bioinform., 2011

<i>survcomp</i>: an R/Bioconductor package for performance assessment and comparison of survival models.
Bioinform., 2011

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.
Bioinform., 2011

Defining an informativeness metric for clustering gene expression data.
Bioinform., 2011

RNA-Seq analysis in MeV.
Bioinform., 2011

GeneSigDB - a curated database of gene expression signatures.
Nucleic Acids Res., 2010

AI Methods for Analyzing Microarray Data.
Proceedings of the Encyclopedia of Artificial Intelligence (3 Volumes), 2009

Decomposition of Gene Expression State Space Trajectories.
PLoS Comput. Biol., 2009

Data-driven normalization strategies for high-throughput quantitative RT-PCR.
BMC Bioinform., 2009

An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation).
BMC Bioinform., 2009

Papers on normalization, variable selection, classification or clustering of microarray data.
Bioinform., 2009

Bioinform., 2009

Session Introduction.
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

Seeded Bayesian Networks: Constructing genetic networks from microarray data.
BMC Syst. Biol., 2008

Session Introduction.
Proceedings of the Biocomputing 2008, 2008

Microarray blob-defect removal improves array analysis.
Bioinform., 2007

Stochasticity and Networks in Genomic Data.
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

The TIGR Maize Database.
Nucleic Acids Res., 2006

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
BMC Bioinform., 2006

It is time to end the patenting of software.
Bioinform., 2006

The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.
Nucleic Acids Res., 2005

CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data.
Bioinform., 2005

MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms.
Bioinform., 2005

The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists.
Nucleic Acids Res., 2003

TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.
Bioinform., 2003

Knowledge-Based Access to the Bio-Medical Literature, Ontologically-Grounded Experiments for the TREC 2003 Genomics Track.
Proceedings of The Twelfth Text REtrieval Conference, 2003

Microarray gene expression data analysis - a beginner's guide.
Blackwell, ISBN: 978-1-40510-682-5, 2003

Genesis: cluster analysis of microarray data.
Bioinform., 2002

An open letter to the scientific journals.
Bioinform., 2002

The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species.
Nucleic Acids Res., 2001

The TIGR Gene Indices: reconstruction and representation of expressed gene sequences.
Nucleic Acids Res., 2000